I have the exact same problem as well. Never used to happen with Quartus v11.0.
It happens about once every few hours of editing, I have not been able to reproduce it. Seems to typically happen when I highlight text and try to change it quickly.
The Altera Knowledge base has two support "solutions" for what may be this issue. Apparently it has to do with highlighting numbers.
See Solution ID rd08062012_329
http://www.altera.com/support/kdb/solutions/rd08062012_329.html And also Solution ID rd07272012_758
http://www.altera.com/support/kdb/solutions/rd07272012_758.html The first of those suggests a fix that I will try.